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            <h1 id="seo-header">【迁移】cellranger定量：One Library, Multiple Flowcells</h1>
            
              <p id="updated-time" class="note note-info" style="">
                
                  
                    Last updated on March 19, 2024 pm
                  
                
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              <div class="markdown-body">
                
                <h2 id="重命名R1、R2">重命名R1、R2</h2>
<ul>
<li><a href="/shi-yong-GATK-zhao-SNP#fastp%E4%B8%80%E9%94%AE%E8%B4%A8%E6%8E%A7">原始数据质控</a></li>
</ul>
<h3 id="重命名前">重命名前</h3>
<p>├── SRR12391722<br>
│ ├── SRR12391722_1.fastq.gz<br>
│ └── SRR12391722_2.fastq.gz<br>
├── SRR12391723<br>
│ ├── SRR12391723_1.fastq.gz<br>
│ └── SRR12391723_2.fastq.gz<br>
├── SRR12391724<br>
│ ├── SRR12391724_1.fastq.gz<br>
│ └── SRR12391724_2.fastq.gz<br>
└── SRR12391725<br>
│├── SRR12391725_1.fastq.gz<br>
│└── SRR12391725_2.fastq.gz</p>
<h3 id="重命名后">重命名后</h3>
<p>SRX8890106<br>
├── SRX8890106_S1_L001_R1_001.fastq.gz<br>
├── SRX8890106_S1_L001_R2_001.fastq.gz<br>
├── SRX8890106_S1_L002_R1_001.fastq.gz<br>
├── SRX8890106_S1_L002_R2_001.fastq.gz<br>
├── SRX8890106_S1_L003_R1_001.fastq.gz<br>
├── SRX8890106_S1_L003_R2_001.fastq.gz<br>
├── SRX8890106_S1_L004_R1_001.fastq.gz<br>
└── SRX8890106_S1_L004_R2_001.fastq.gz</p>
<h2 id="进行定量">进行定量</h2>
<p><a href="https://hexo.limour.top/go/#aHR0cHM6Ly9zdXBwb3J0LjEweGdlbm9taWNzLmNvbS9zaW5nbGUtY2VsbC1nZW5lLWV4cHJlc3Npb24vc29mdHdhcmUvcGlwZWxpbmVzL2xhdGVzdC91c2luZy90dXRvcmlhbF9jdA==" rel="noopener external nofollow noreferrer">Running cellranger count</a>; <a href="https://hexo.limour.top/go/#aHR0cHM6Ly9zdXBwb3J0LjEweGdlbm9taWNzLmNvbS9zaW5nbGUtY2VsbC1nZW5lLWV4cHJlc3Npb24vc29mdHdhcmUvcGlwZWxpbmVzL2xhdGVzdC9pbnN0YWxsYXRpb24=" rel="noopener external nofollow noreferrer">cellranger 安装</a></p>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-meta">#!/bin/bash</span><br><span class="hljs-built_in">export</span> PATH=/opt/cellranger/cellranger-6.1.2:<span class="hljs-variable">$PATH</span><br>db=/opt/cellranger/refdata-gex-GRCh38-2020-A<br>data=/home/jovyan/work_st/sce/GSE137829/data<br>work=/home/jovyan/work_st/sce/GSE137829/res<br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$work</span><br><span class="hljs-built_in">cd</span> <span class="hljs-variable">$work</span><br><span class="hljs-keyword">for</span> sample <span class="hljs-keyword">in</span> <span class="hljs-variable">$&#123;data&#125;</span>/*;<br><span class="hljs-keyword">do</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$sample</span><br>sample_res=<span class="hljs-variable">$&#123;sample##*/&#125;</span><br>cellranger count --<span class="hljs-built_in">id</span>=<span class="hljs-variable">$sample_res</span> \<br>--localcores=12 \<br>--transcriptome=<span class="hljs-variable">$db</span> \<br>--fastqs=<span class="hljs-variable">$sample</span> \<br>--sample=<span class="hljs-variable">$sample_res</span> \<br>--expect-cells=5000<br><span class="hljs-keyword">done</span><br></code></pre></td></tr></table></figure>
<ul>
<li>nano <a href="https://hexo.limour.top/go/#aHR0cDovLzEwMy5zaA==" rel="noopener external nofollow noreferrer">103.sh</a></li>
<li>chmod +x <a href="https://hexo.limour.top/go/#aHR0cDovLzEwMy5zaA==" rel="noopener external nofollow noreferrer">103.sh</a></li>
<li>./103.sh</li>
</ul>
<h2 id="附加：scVelo-细胞轨迹">附加：scVelo 细胞轨迹</h2>
<h3 id="安装依赖">安装依赖</h3>
<h4 id="cellranger">cellranger</h4>
<p>GRCh38_rmsk.gtf.gz：<a href="https://hexo.limour.top/go/#aHR0cHM6Ly9nZW5vbWUudWNzYy5lZHUvY2dpLWJpbi9oZ1RhYmxlcz9oZ3NpZD02MTE0NTQxMjdfTnR2bGFXNnhCU0lSWUpFQkkwaVJERVdpc0lUYSZhbXA7Y2xhZGU9bWFtbWFsJmFtcDtvcmc9SHVtYW4mYW1wO2RiPTAmYW1wO2hndGFfZ3JvdXA9YWxsVHJhY2tzJmFtcDtoZ3RhX3RyYWNrPXJtc2smYW1wO2hndGFfdGFibGU9cm1zayZhbXA7aGd0YV9yZWdpb25UeXBlPWdlbm9tZSZhbXA7cG9zaXRpb249JmFtcDtoZ3RhX291dHB1dFR5cGU9Z2ZmJmFtcDtoZ3RhX291dEZpbGVOYW1lPUdSQ2gzOF9ybXNrLmd0Zg==" rel="noopener external nofollow noreferrer">https://genome.ucsc.edu/cgi-bin/hgTables</a></p>
<p><img src="https://img.limour.top/2023/09/01/64f1cf9a391ae.webp" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt=""></p>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-built_in">cd</span> /opt/cellranger<br>wget &lt;Cell Ranger&gt;<br>wget &lt;References&gt;<br>tar -xzvf cellranger-6.1.2.tar.gz<br>tar -xzvf refdata-gex-GRCh38-2020-A.tar.gz<br>下载 GRCh38_rmsk.gtf.gz 上传阿里云盘<br>./aliyunpan<br>login<br>d GRCh38_rmsk.gtf.gz -saveto /opt/cellranger<br>gunzip GRCh38_rmsk.gtf.gz<br><span class="hljs-built_in">export</span> PATH=/opt/cellranger/cellranger-6.1.2:<span class="hljs-variable">$PATH</span><br>cellranger sitecheck &gt; sitecheck.txt<br>cellranger upload xxx@fudan.edu.cn sitecheck.txt<br>cellranger testrun --<span class="hljs-built_in">id</span>=tiny<br>cellranger upload xxx@fudan.edu.cn tiny/tiny.mri.tgz<br></code></pre></td></tr></table></figure>
<h4 id="velocyto">velocyto</h4>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda create -n velocyto -c conda-forge python=3.7 -y<br>conda activate velocyto<br>conda install numpy scipy cython numba matplotlib scikit-learn h5py click -y<br>pip install pysam<br>pip install velocyto<br>velocyto --<span class="hljs-built_in">help</span><br>conda install -c bioconda samtools=1.15.1 -y<br></code></pre></td></tr></table></figure>
<h4 id="scVelo">scVelo</h4>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda install -c conda-forge widgetsnbextension -y<br>jupyter nbextension <span class="hljs-built_in">enable</span> --py widgetsnbextension<br><span class="hljs-comment"># 重启 jupyter</span><br>conda create -n scVelo -c conda-forge python=3.7 -y<br>conda activate scVelo<br>conda install -c conda-forge scanpy -y<br>conda install -c conda-forge matplotlib -y<br>pip install -U scvelo<br>pip install -U tqdm ipywidgets<br>conda install -c conda-forge ipykernel -y<br>python -m ipykernel install --user --name python-scVelo<br></code></pre></td></tr></table></figure>
<h3 id="准备1：运行-cellranger">准备1：运行 cellranger</h3>
<p>data<br>
├── hPB003<br>
│ ├── hPB003_S1_L001_R1_001.fastq.gz<br>
│ └── hPB003_S1_L001_R2_001.fastq.gz<br>
├── hPB004<br>
│ ├── hPB004_S1_L001_R1_001.fastq.gz<br>
│ └── hPB004_S1_L001_R2_001.fastq.gz<br>
├── hPB005<br>
│ ├── hPB005_S1_L001_R1_001.fastq.gz<br>
│ └── hPB005_S1_L001_R2_001.fastq.gz<br>
├── hPB006<br>
│ ├── hPB006_S1_L001_R1_001.fastq.gz<br>
│ └── hPB006_S1_L001_R2_001.fastq.gz<br>
└── hPB007<br>
├── hPB007_S1_L001_R1_001.fastq.gz<br>
└── hPB007_S1_L001_R2_001.fastq.gz</p>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-meta">#!/bin/bash</span><br><span class="hljs-built_in">export</span> PATH=/opt/cellranger/cellranger-6.1.2:<span class="hljs-variable">$PATH</span><br>db=/opt/cellranger/refdata-gex-GRCh38-2020-A<br>data=/home/jovyan/upload/zl_liu/data/data/data<br>work=/home/jovyan/upload/zl_liu/data/data/res<br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$work</span><br><span class="hljs-built_in">cd</span> <span class="hljs-variable">$work</span><br><span class="hljs-keyword">for</span> sample <span class="hljs-keyword">in</span> <span class="hljs-variable">$&#123;data&#125;</span>/*;<br><span class="hljs-keyword">do</span> <span class="hljs-built_in">echo</span> <span class="hljs-variable">$sample</span><br>sample_res=<span class="hljs-variable">$&#123;sample##*/&#125;</span><br>cellranger count --<span class="hljs-built_in">id</span>=<span class="hljs-variable">$sample_res</span> \<br>--localcores=4 \<br>--transcriptome=<span class="hljs-variable">$db</span> \<br>--fastqs=<span class="hljs-variable">$sample</span> \<br>--sample=<span class="hljs-variable">$sample_res</span> \<br>--expect-cells=5000<br><span class="hljs-keyword">done</span><br></code></pre></td></tr></table></figure>
<h3 id="准备2：从cellranger得到loom文件">准备2：从cellranger得到loom文件</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda activate velocyto<br><span class="hljs-comment">#!/bin/bash</span><br>db=/opt/cellranger/refdata-gex-GRCh38-2020-A<br>work=/home/jovyan/upload/zl_liu/data/data/res<br>rmsk_gtf=/opt/cellranger/GRCh38_rmsk.gtf <span class="hljs-comment"># 从genome.ucsc.edu下载 </span><br>cellranger_gtf=<span class="hljs-variable">$&#123;db&#125;</span>/genes/genes.gtf<br><span class="hljs-built_in">ls</span> -lh <span class="hljs-variable">$rmsk_gtf</span>  <span class="hljs-variable">$work</span> <span class="hljs-variable">$cellranger_gtf</span><br><span class="hljs-keyword">for</span> sample <span class="hljs-keyword">in</span> <span class="hljs-variable">$&#123;work&#125;</span>/*;<br><span class="hljs-keyword">do</span> <span class="hljs-built_in">echo</span> <span class="hljs-variable">$sample</span><br>velocyto run10x -m <span class="hljs-variable">$rmsk_gtf</span> <span class="hljs-variable">$sample</span> <span class="hljs-variable">$cellranger_gtf</span><br><span class="hljs-keyword">done</span><br></code></pre></td></tr></table></figure>
<h3 id="准备3：从-Seurat-输出-标注-和-UMAP">准备3：从 Seurat 输出 标注 和 UMAP</h3>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs r">library<span class="hljs-punctuation">(</span>Seurat<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>tidyverse<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>stringr<span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;~/upload/zl_liu/data/pca.rds&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br></pre></td><td class="code"><pre><code class="hljs r">f_scVelo_group_by <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>n <span class="hljs-keyword">in</span> unique<span class="hljs-punctuation">(</span><span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> df<span class="hljs-punctuation">[</span>df<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">==</span> n<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>f_scVelo_get_reduction <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">,</span> cell.embeddings<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>n <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        dfl<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> cell.embeddings<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    dfl<br><span class="hljs-punctuation">&#125;</span><br>f_scVelo_str_extract_rowN <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">,</span> grepP<span class="hljs-operator">=</span><span class="hljs-string">&#x27;(?=.&#123;10&#125;)([AGCT]&#123;16&#125;)(?=-1)&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>n <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        rownames<span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> str_extract<span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> grepP<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    dfl<br><span class="hljs-punctuation">&#125;</span><br><br>test <span class="hljs-operator">&lt;-</span> f_scVelo_group_by<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">[[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;patient_id&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;cell_type_fig3&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;patient_id&#x27;</span><span class="hljs-punctuation">)</span><br>test <span class="hljs-operator">&lt;-</span> f_scVelo_get_reduction<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> sce<span class="hljs-operator">@</span>reductions<span class="hljs-operator">$</span>umap<span class="hljs-operator">@</span>cell.embeddings<span class="hljs-punctuation">)</span><br>test <span class="hljs-operator">&lt;-</span> f_scVelo_get_reduction<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> sce<span class="hljs-operator">@</span>reductions<span class="hljs-operator">$</span>pca<span class="hljs-operator">@</span>cell.embeddings<span class="hljs-punctuation">)</span><br>test <span class="hljs-operator">&lt;-</span> f_scVelo_str_extract_rowN<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br></pre></td><td class="code"><pre><code class="hljs r">f_scVelo_label_reduction <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">,</span> workdir<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">,</span> outDir<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    outDir <span class="hljs-operator">=</span> file.path<span class="hljs-punctuation">(</span>workdir<span class="hljs-punctuation">,</span> outDir<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;velocyto&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;metadata.csv&#x27;</span><span class="hljs-punctuation">)</span><br>    write.csv<span class="hljs-punctuation">(</span>dfl<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> outDir<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br><br>work<span class="hljs-operator">=</span><span class="hljs-string">&#x27;/home/jovyan/upload/zl_liu/data/data/res&#x27;</span><br>f_scVelo_label_reduction<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> work<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;patient1&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;hPB003&#x27;</span><span class="hljs-punctuation">)</span><br>f_scVelo_label_reduction<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> work<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;patient3&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;hPB004&#x27;</span><span class="hljs-punctuation">)</span><br>f_scVelo_label_reduction<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> work<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;patient4&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;hPB006&#x27;</span><span class="hljs-punctuation">)</span><br>f_scVelo_label_reduction<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> work<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;patient5&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;hPB007&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h3 id="运行1-合并数据">运行1: 合并数据</h3>
<h4 id="第一步-导入模块">第一步 导入模块</h4>
<figure class="highlight python"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br></pre></td><td class="code"><pre><code class="hljs python"><span class="hljs-keyword">import</span> scvelo <span class="hljs-keyword">as</span> scv<br><span class="hljs-keyword">import</span> scanpy <span class="hljs-keyword">as</span> sc<br><span class="hljs-keyword">import</span> numpy <span class="hljs-keyword">as</span> np<br><span class="hljs-keyword">import</span> pandas <span class="hljs-keyword">as</span> pd<br><span class="hljs-keyword">import</span> seaborn <span class="hljs-keyword">as</span> sns <br>scv.settings.verbosity = <span class="hljs-number">3</span>  <span class="hljs-comment"># show errors(0), warnings(1), info(2), hints(3)</span><br>scv.settings.set_figure_params(<span class="hljs-string">&#x27;scvelo&#x27;</span>)  <span class="hljs-comment"># for beautified visualization</span><br></code></pre></td></tr></table></figure>
<h4 id="第二步-读取数据（时间很长）">第二步 读取数据（时间很长）</h4>
<figure class="highlight python"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs python">loomf = <span class="hljs-string">&#x27;/home/jovyan/upload/zl_liu/data/data/res/hPB003/velocyto/hPB003.loom&#x27;</span><br>adata = scv.read(loomf, cache=<span class="hljs-literal">False</span>)<br>metadataf = <span class="hljs-string">&#x27;/home/jovyan/upload/zl_liu/data/data/res/hPB003/velocyto/metadata.csv&#x27;</span><br>meta = pd.read_csv(metadataf, index_col=<span class="hljs-number">0</span>)<br></code></pre></td></tr></table></figure>
<h4 id="第三步-取交集并合并数据">第三步 取交集并合并数据</h4>
<figure class="highlight python"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><code class="hljs python">tmp = [x <span class="hljs-keyword">for</span> x <span class="hljs-keyword">in</span>  (x[<span class="hljs-number">7</span>:<span class="hljs-number">23</span>] <span class="hljs-keyword">for</span> x <span class="hljs-keyword">in</span> adata.obs.index) <span class="hljs-keyword">if</span> x <span class="hljs-keyword">in</span> meta.index]<br>meta = meta.loc[tmp]<br>adata = adata[[<span class="hljs-string">f&#x27;hPB003:<span class="hljs-subst">&#123;x&#125;</span>x&#x27;</span> <span class="hljs-keyword">for</span> x <span class="hljs-keyword">in</span> tmp]]<br><br>test = meta[<span class="hljs-string">&#x27;cell_type_fig3&#x27;</span>]<br>test.index = adata.obs.index<br>adata.obs[<span class="hljs-string">&#x27;cell_type_fig3&#x27;</span>] = test<br><br>adata.obsm[<span class="hljs-string">&#x27;X_pca&#x27;</span>] =  np.asarray(meta.iloc[:, <span class="hljs-number">4</span>:])<br>adata.obsm[<span class="hljs-string">&#x27;X_umap&#x27;</span>] = np.asarray(meta.iloc[:, <span class="hljs-number">2</span>:<span class="hljs-number">4</span>])<br><br>sc.pl.pca(adata, color=<span class="hljs-string">&#x27;cell_type_fig3&#x27;</span>)<br>sc.pl.umap(adata, color=<span class="hljs-string">&#x27;cell_type_fig3&#x27;</span>)<br></code></pre></td></tr></table></figure>
<h3 id="运行2-计算绘图">运行2: 计算绘图</h3>
<h4 id="计算">计算</h4>
<figure class="highlight python"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><code class="hljs python">scv.pp.moments(adata, n_pcs=<span class="hljs-number">30</span>, n_neighbors=<span class="hljs-number">30</span>)<br><br>scv.tl.recover_dynamics(adata, n_jobs=<span class="hljs-number">8</span>)<br><br>scv.tl.velocity(adata, mode=<span class="hljs-string">&#x27;dynamical&#x27;</span>)<br><br>scv.tl.velocity_graph(adata, n_jobs=<span class="hljs-number">8</span>)<br><br>adata.write(<span class="hljs-string">&#x27;hPB003.h5ad&#x27;</span>)<br></code></pre></td></tr></table></figure>
<h4 id="绘图">绘图</h4>
<figure class="highlight python"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs python"><span class="hljs-keyword">from</span> matplotlib.pyplot <span class="hljs-keyword">import</span> rc_context<br><span class="hljs-keyword">with</span> rc_context(&#123;<span class="hljs-string">&#x27;figure.figsize&#x27;</span>: (<span class="hljs-number">12</span>, <span class="hljs-number">12</span>)&#125;):<br>    scv.pl.velocity_embedding_stream(adata, basis=<span class="hljs-string">&#x27;umap&#x27;</span>, color=[<span class="hljs-string">&#x27;cell_type_fig3&#x27;</span>], save = <span class="hljs-string">&quot;hPB003 velocity embedding stream.svg&quot;</span>)<br></code></pre></td></tr></table></figure>
<p><img src="https://img.limour.top/2023/09/01/64f1d34304c5a.webp" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="细胞分化轨迹图"></p>

                
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        <a href="/tags/cellranger/" class="print-no-link">#cellranger</a>
      
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      <div>【迁移】cellranger定量：One Library, Multiple Flowcells</div>
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